Introduction to version control with Git

Day 1: Concepts and a basic workflow

Selina Baldauf

September 18, 2023

Who am I?

Scientific programmer @ theoretical ecology group

What do you want to learn here?

Aims of the workshop

Git is a huge topic and Git is very powerful.

Learn simple Git workflows in theory and practice that you can immediately apply to your research projects.

Topics

Today 2.30 - 4 pm

  • Introduction to Git concepts
  • Simple Git workflow for your own projects

Tomorrow 2.30 - 4 pm

  • Collaborate using Git and Github

Next Monday 2.30 - 3.30 pm

  • Until then: work with Git on your own projects
  • Q&A
  • Advanced topics

Organization

  • Material is all online

  • Certificate of attendance from the graduate center

  • Feedback is very welcome

  • Just interrupt me for questions/comments

Before we start

Did anyone have problems with the workshop preparation?

  • Install Git
  • Install Github Desktop
  • Get a Github account and connect it with Github Desktop

Let’s get started

Why version control?

Two examples in which proper version control can be a time/stress saver

Version control with Git

  • Complete and long-term history of every file in your project

  • Open source and free to use version control software

  • Quasi standard for software development

  • A whole universe of other software and services around it

Version control with Git

  • For projects with mainly text files (e.g. code, markdown files, …)

  • Basic idea: Take snapshots (commits) of your project over time

  • A project version controlled with Git is a Git repository (repo)

Version control with Git

Git is a distributed version control system

  • Idea: many local repositories synced via one remote repo
  • Everyone has a complete copy of the repo

How to use Git

After you installed it there are different ways to interact with the software.

How to use Git - Terminal

Using Git from the terminal

➕ Most control

➕ A lot of help/answers online

➖ You need to use terminal 😱

How to use Git - Integrated GUIs

A Git GUI is integrated in most (all?) IDEs, e.g. R Studio, VS Code

➕ Easy and intuitive

➕ Stay inside IDE

➖ Different for every program

How to use Git - Standalone GUIs

Standalone Git GUI software, e.g. Github Desktop, Source Tree, …

➕ Easy and intuitive

➕ Use for all projects

➖ Switch programs to use Git

How to use Git

Which one to choose?

  • Depends on experience and taste
  • You can mix methods because they are all interfaces to the same Git
  • We will use Github Desktop
    • Beginner-friendly, intuitive and convenient
    • Nice integration with Github

Tip

Have a look at the website where you find How-To guides for the other methods as well.

The basic Git workflow

git init, git add, git commit, git push

Example

A cook book project to collect all my favorite recipes.

Step 1: Initialize a Git repository

Step 1: Initialize a Git repository

Step 1: Initialize a Git repository

Step 2: Add and modify files

Git detects any changes in the working directory

Step 2: Stage changes

Staging a file means to list it for the next commit.

Step 3: Commit changes

  • Commits are the snapshots of your project state

Step 3: Commit changes

  • Changes are part of Git history and staging area is clear again

How to write good commit messages?

xkcd on commit messages

How to write good commit messages?

✔️

Add pie recipe

This is my favorite pie in the world. 
The recipe comes from my grandfather and 
he learned it from his neighbor.

❌

added a file.

This is a a really good recipe that I like.

See here for more details but some general rules:

  1. Limit summary line to 50 characters
  2. Capitalize summary line
  3. Do not end summary line with period
  4. Use imperative mood in the subject line
  5. Use the Description to explain what and why, not how

Now you

Start your own cook book
Complete task 1 “Local repo” (10 min)

Stay in the meeting for the task.
Ask if you are stuck.
Turn down/off volume if you are disturbed.

The commit history

 

Step 4: Share changes with the remote repo

  • Use remote repos (on a server) to synchronize, share and collaborate

  • Remote repos can be private (you + collaborators) or public (visible to anyone)

Step 4: Share changes with the remote repo

Different remote repositories

  • There are commercial and self-hosted options for your remote repositories
    • Commercial: Github, Gitlab, Bitbucket, …
    • Self-hosted: Gitlab (maybe at your institution?)
  • Please be aware of your institutional guidelines
    • Servers outside EU
    • Privacy rules might apply

Now you

Publish your cook book on Github
Complete task 2 “Github” (5 min)

Summary of the basic steps

  • git init: Initialize a git repository
    • Adds a .git folder to your working directory
  • git add: Add files to the staging area
    • This marks the files as being part of the next commit
  • git commit: Take a snapshot of your current project version
    • Includes time stamp, commit message and information on the person who did the commit
  • git push: Push new commits to the remote repository
    • Sync your local project version with the remote e.g. on Github

Undo things

git revert

Revert changes

  • Use git revert to revert specific commits
  • This does not delete the commit, it creates a new commit that undoes a previous commit
    • It’s a safe way to undo commited changes

Now you

Revert a part of your recipe
Complete the task 3 “Time travel” (5 min)

Publish your repositories

Publish your repositories

Github/Gitlab are a good way to publish and share your work.

Advantages of publishing your code
  • Others can build on your work
  • Citations
  • Reproducibility
  • Get feedback

Publish your repositories

You can increase the quality/complexity of your repo by

Thanks for your attention

Questions?

Go back in time

git checkout

Checkout a previous commit

  • Bring your work space back in time temporarily with git checkout

Ignoring files

Ignore files with .gitignore

  • Create a file with the name .gitignore in working directory

  • Add all files and directories you want to ignore to the .gitignore file

  • Useful to ignore e.g.
    • Compiled code and build directories
    • Log files
    • Hidden system files
    • Personal IDE config files
    • …

Ignore files with .gitignore

  • Create a file with the name .gitignore in working directory

  • Add all files and directories you want to ignore to the .gitignore file

Example

*.html    # ignore all .html files
*.pdf     # ignore all .pdf files

debug.log # ignore the file debug.log

build/    # ignore all files in subdirectory build

See here for more ignore patterns that you can use.

Preparation for tomorrow

  • Tomorow we have teams of 2
  • Collaborate on the cook book of your team mate

Now please

  1. Enter your Github Account Name and the link to your repo here
  2. Look for the Github Name of your team mate and add them as a collaborator to your repository
  3. Accept the invitation of your team mate to their repository
  • You will get an Email or you can do it on Github

Basic Git workflow